Just a little update on this strange issue.
I spent a lot of time checking every single component in the ignition system, along with checking resistance in every wire. What I came up with is first a faulty tach, and second and faulty/iffy ESA module. The tach I can't explain, except when it was connected, all of the problems were there with either the ESA module or when it was wired like a Mercruiser. I robbed one of my friends boats and installed his tach and all issues went away. I'll have to source a new tach and give his back.
I thought it was fixed after the new tach, but as the boat heated up, the ESA started to not work. Tested everything again, and it has to be the module. I cut the connectors off of the module and built a harness to just use the ESA switch so all I have to do is plug the new module in. After a entire day on the water with the module bypassed, everything worked great. I'll order a new module and get it back to factory this week.
I just want to say thank you for all of the help, you guys are great. Thanks, Justin.